install.packages('meteR') # we're live on CRAN!
devtools::install_github('cmerow/meteR') # dev version
library(meteR)

data(arth)
head(arth, n = 3)

##        spp count   mass
## 1 blacchel     1 4.7480
## 2 mecyocul     1 1.6490
## 3 eurynsp1     1 0.2584

data(arth)
head(arth, n = 3)

##        spp count   mass
## 1 blacchel     1 4.7480
## 2 mecyocul     1 1.6490
## 3 eurynsp1     1 0.2584

arthESF <- meteESF(spp = arth$spp, abund = arth$count, 
                   power = arth$mass^0.75)
arthESF # this is the print method

## METE object with state variables:
##       S0       N0       E0 
##    76.00   547.00 15868.26 
## 
## with Lagrange multipliers:
##         la1         la2 
## 0.037929267 0.004960427

length(unique(arth$spp))

## [1] 76

sum(arth$count)

## [1] 547

sum(arth$mass^0.75 / min(arth$mass^0.75))

## [1] 15868.26

length(unique(arth$spp))

## [1] 76

sum(arth$count)

## [1] 547

sum(arth$mass^0.75 / min(arth$mass^0.75))

## [1] 15868.26

arthESF_stateVar <- meteESF(S0 = 76, N0 = 547, E0 = 15868.26)

data(anbo)
head(anbo, n = 3)

##   row column    spp count
## 1   3      3   cabr     3
## 2   3      3 caspi1    20
## 3   3      3   crcr     3

data(anbo)
head(anbo, n = 3)

##   row column    spp count
## 1   3      3   cabr     3
## 2   3      3 caspi1    20
## 3   3      3   crcr     3

anboSSF <- meteSSF(spp = anbo$spp, sppID = 'gnwe', 
                   abund = anbo$count, row = anbo$row, 
                   col = anbo$column, A = 1, A0 = 16)
anboSSF

## METE object with state variables:
## n0  A A0 
## 41  1 16 
## 
## with Lagrange multipliers:
## [1] 0.3294792

arthSAD <- sad(arthESF)

arthSAD <- sad(arthESF)
plot(arthSAD, ptype = 'rad')

arthSAD <- sad(arthESF)
plot(arthSAD, ptype = 'rad')

logLik(arthSAD)

## 'log Lik.' -201.8189 (df=2)

anboSAR <- meteSAR(spp = anbo$spp, abund = anbo$count, 
                   row = anbo$row, col = anbo$col, 
                   Amin = 1, A0 = 16)
plot(anboSAR)

anboSAR <- meteSAR(spp = anbo$spp, abund = anbo$count, 
                   row = anbo$row, col = anbo$col, 
                   Amin = 1, A0 = 16)
plot(anboSAR)

mse(anboSAR)

## [1] 29.79903